Alfred Simkin
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View article: COATswga: A Coverage Optimizing and Accurate Toolkit for fast primer design in selective whole genome amplification
COATswga: A Coverage Optimizing and Accurate Toolkit for fast primer design in selective whole genome amplification Open
Background Despite the transformative nature of next-generation sequencing in genomics, efficiently capturing underrepresented microbial DNA from complex biological mixtures, such as pathogens from host samples, remains a persistent challe…
View article: Towards an open analysis ecosystem for<i>Plasmodium</i>genomic epidemiology
Towards an open analysis ecosystem for<i>Plasmodium</i>genomic epidemiology Open
Major advances in Plasmodium sequencing approaches, bioinformatic pipelines, and data analysis tools have provided valuable insights into malaria epidemiology from parasite genomic data. However, translating genetic data into actionable in…
View article: Capsid transfer of the retrotransposon Copia controls structural synaptic plasticity in Drosophila
Capsid transfer of the retrotransposon Copia controls structural synaptic plasticity in Drosophila Open
Transposons are parasitic genome elements that can also serve as raw material for the evolution of new cellular functions. However, how retrotransposons are selected and domesticated by host organisms to modulate synaptic plasticity remain…
View article: Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon
Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon Open
Background: Resistance to antimalarial drugs remains a major obstacle to malaria elimination. Multiplexed, targeted amplicon sequencing is being adopted for surveilling resistance and dissecting the genetics of complex malaria infections. …
View article: Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon
Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon Open
Background Resistance to antimalarial drugs remains a major obstacle to malaria elimination. Multiplexed, targeted amplicon sequencing is being adopted for surveilling resistance and dissecting the genetics of complex malaria infections. M…
View article: Emergence and Rising Prevalence of Artemisinin Partial Resistance Marker Kelch13 P441L in a Low Malaria Transmission Setting in Southern Zambia
Emergence and Rising Prevalence of Artemisinin Partial Resistance Marker Kelch13 P441L in a Low Malaria Transmission Setting in Southern Zambia Open
Increasing artemisinin partial resistance (ArtR) due to mutations in the gene encoding Kelch13 ( Pfk13 ) protein in eastern Africa is of urgent concern, and mutations, such as Pfk13 P441L, continue to emerge. We used an amplicon deep-seque…
View article: Population genomics of Plasmodium ovale species in sub-Saharan Africa
Population genomics of Plasmodium ovale species in sub-Saharan Africa Open
View article: High-throughput genotyping of Plasmodium vivax in the Peruvian Amazon via molecular inversion probes
High-throughput genotyping of Plasmodium vivax in the Peruvian Amazon via molecular inversion probes Open
View article: Population genomics of Plasmodium ovale species in sub-Saharan Africa
Population genomics of Plasmodium ovale species in sub-Saharan Africa Open
View article: High-throughput genotyping of Plasmodium vivax in the Peruvian Amazon via molecular inversion probes
High-throughput genotyping of Plasmodium vivax in the Peruvian Amazon via molecular inversion probes Open
View article: Application of a new highly multiplexed amplicon sequencing tool to evaluate<i>Plasmodium falciparum</i>antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon
Application of a new highly multiplexed amplicon sequencing tool to evaluate<i>Plasmodium falciparum</i>antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon Open
Background Resistance to antimalarial drugs remains a major obstacle to malaria elimination. Multiplexed, targeted amplicon sequencing is being adopted for surveilling resistance and dissecting the genetics of complex malaria infections. M…
View article: Population Genomics of<i>Plasmodium malariae</i>from Four African Countries
Population Genomics of<i>Plasmodium malariae</i>from Four African Countries Open
Plasmodium malariae is geographically widespread but neglected and may become more prevalent as P. falciparum declines. We completed the largest genomic study of African P. malariae to-date by performing hybrid capture and sequencing of 77…
View article: Prevalence of mutations associated with artemisinin partial resistance and sulfadoxine–pyrimethamine resistance in 13 regions in Tanzania in 2021: a cross-sectional survey
Prevalence of mutations associated with artemisinin partial resistance and sulfadoxine–pyrimethamine resistance in 13 regions in Tanzania in 2021: a cross-sectional survey Open
This study was funded by the Bill & Melinda Gates Foundation and the National Institutes of Health.
View article: High-Throughput Genotyping of <i>Plasmodium vivax</i> in the Peruvian Amazon via Molecular Inversion Probes
High-Throughput Genotyping of <i>Plasmodium vivax</i> in the Peruvian Amazon via Molecular Inversion Probes Open
Plasmodium vivax transmission occurs throughout the tropics and is an emerging threat in areas of Plasmodium falciparum decline, causing relapse infections that complicate treatment and control. Targeted sequencing for P. falciparum has be…
View article: Population genomics of<i>Plasmodium ovale</i>species in sub-Saharan Africa
Population genomics of<i>Plasmodium ovale</i>species in sub-Saharan Africa Open
Plasmodium ovale curtisi ( Poc) and Plasmodium ovale wallikeri ( Pow ) are relapsing malaria parasites endemic to Africa and Asia that were previously thought to represent a single species. Amid increasing detection of ovale malaria in sub…
View article: Dueling Endogenous Viral-Like Sequences Control Synaptic Plasticity
Dueling Endogenous Viral-Like Sequences Control Synaptic Plasticity Open
The function of a large part of most genomes, generally called “junk DNA”, remains largely unknown. Much of this enigmatic DNA corresponds to transposons, which are considered genomic parasites. Here, we show the protein of the Ty1 retrotr…
View article: Country wide surveillance reveals prevalent artemisinin partial resistance mutations with evidence for multiple origins and expansion of high level sulfadoxine-pyrimethamine resistance mutations in northwest Tanzania
Country wide surveillance reveals prevalent artemisinin partial resistance mutations with evidence for multiple origins and expansion of high level sulfadoxine-pyrimethamine resistance mutations in northwest Tanzania Open
Background Emergence of artemisinin partial resistance (ART-R) in Plasmodium falciparum is a growing threat to the efficacy of artemisinin combination therapies (ACT) and the efforts for malaria elimination. The emergence of Plasmodium fal…
View article: Evolutionary dynamics of microRNA target sites across vertebrate evolution
Evolutionary dynamics of microRNA target sites across vertebrate evolution Open
MicroRNAs (miRNAs) control the abundance of the majority of the vertebrate transcriptome. The recognition sequences, or target sites, for bilaterian miRNAs are found predominantly in the 3' untranslated regions (3'UTRs) of mRNAs, and are a…
View article: Evolutionary Dynamics of microRNA target sites across vertebrate evolution
Evolutionary Dynamics of microRNA target sites across vertebrate evolution Open
MicroRNAs (miRNAs) control the abundance of the majority of the vertebrate transcriptome. The recognition sequences, or target sites, for bilaterian miRNAs are found predominantly in the 3′ untranslated regions (3′UTRs) of mRNAs, and are a…
View article: A widespread sequence-specific mRNA decay pathway mediated by hnRNPs A1 and A2/B1
A widespread sequence-specific mRNA decay pathway mediated by hnRNPs A1 and A2/B1 Open
3′-untranslated regions (UTRs) specify post-transcriptional fates of mammalian messenger RNAs (mRNAs), yet knowledge of the underlying sequences and mechanisms is largely incomplete. Here, we identify two related novel 3′ UTR motifs in mam…